I just saw a few comments on Cognitive Sciences which were obsolete: someone commented that a reference should be added, and the OP added a reference. Both have placed subsequent comments so I know these comments have been seen.

I flagged both comments as "obsolete" to auto-delete them and also leave a message in the log so my fellow mods would know what I did and why:

Whew. That's a relief @BoltClock! I mean, I still want to be a benevolent dictat-achem... moderator, so I am still wondering if what I did was acceptable. The badge reference was (mostly) a joke :-)
–
The Unhandled ExceptionSep 12 '12 at 22:46

1

Honestly, it's great that you laid it out, but I don't think that's necessary. If the comments were blatantly obsolete, then just wipe them out. If you feel that the action will need the detail later, then do so, but just deleting something for obvious reasons and adding more info to it is less important than other moderator responsibilities.
–
casperOneSep 12 '12 at 22:56

@casperOne I figure that flagging as obsolete is only 2 clicks more than deleting, and the traffic on our site is so slow that it's not like I have a lot of flags to handle...
–
The Unhandled ExceptionSep 12 '12 at 22:58

I was tempted to ask if there was ever possibly a chance in which I should abuse post flags in this fashion but decided I like my diamond too much. Thanks Shog9!
–
The Unhandled ExceptionSep 17 '12 at 2:05

When you (as a moderator) delete a comment, or you flag a comment which is then automatically deleted, a log entry is created in the "most recent moderator's activity" view (admin/history/<moderator-id>), and in both the cases the entry is the same:

Comment deleted: [comment text]

If you just want to leave a log entry, both the actions has the same effect.

It is true that, when you flag a comment, an entry is created in admin/posts/<post-id>/show-flags, but the reason you delete a comment (which is automatically done when a moderator flag a comment) is not an information normally useful to other moderators, and it is not given on users/flagged-posts/<user-id>, which would be the page where probably other moderators would look for having information about the bad behavior of the user.
Take the case you flag as not an answer something that should be written as comment, or that is a completely different question. In this case, you would provide more information to other moderators, who would be able to notice the user wrote X answers instead of commenting, or asking a different question, when looking at users/flagged-posts/<user-id>.

I am not saying that in one case is acceptable, and in the other one is not acceptable. I am saying that in one case you are not giving any helpful information to other users, while you are probably giving useful information in the other case. I imagine that knowing a user wrote X comments that were then obsolete is not an information useful for the moderators, as that is not a reason for banning a user from a site.